Interaction test
- A simple distance-based pruning method is used here, with total window size of 500 kb (250 kb on each side).
Interaction test loci
|
index_var
|
chr
|
pos
|
P_int
|
G-W interaction effect
|
P_joint
|
P_marginal
|
|
rs12136785
|
1
|
89478687
|
4.7e-06
|
FALSE
|
6.70e-06
|
0.0884292
|
|
rs75242550
|
2
|
47777458
|
9.6e-06
|
FALSE
|
3.74e-05
|
0.4243720
|
|
rs12197749
|
6
|
146536288
|
3.1e-06
|
FALSE
|
1.92e-05
|
0.3766780
|
|
7:7343876_CA_C
|
7
|
7343876
|
2.4e-06
|
FALSE
|
7.80e-06
|
0.3709310
|
|
rs4128327
|
8
|
110032847
|
3.4e-06
|
FALSE
|
1.12e-05
|
0.0793897
|
|
rs555728622
|
10
|
100281893
|
5.8e-06
|
FALSE
|
2.62e-05
|
0.8744820
|
|
11:6801573_CAAA_C
|
11
|
6801573
|
9.1e-06
|
FALSE
|
5.60e-06
|
0.1917850
|
|
rs61944504
|
13
|
27321494
|
2.3e-06
|
FALSE
|
1.14e-05
|
0.3039250
|
|
rs4793425
|
17
|
70299527
|
2.9e-06
|
FALSE
|
8.40e-06
|
0.8687370
|
|
rs55690660
|
17
|
72352686
|
6.5e-06
|
FALSE
|
3.83e-05
|
0.5641650
|
|
rs1053744
|
22
|
50885775
|
6.1e-06
|
FALSE
|
1.33e-05
|
0.1111860
|
Joint test
Joint test loci
|
index_var
|
chr
|
pos
|
P
|
Genome-wide joint locus
|
Genome-wide marginal locus
|
|
rs12727804
|
1
|
91733994
|
0
|
TRUE
|
TRUE
|
|
rs17544265
|
1
|
215152131
|
0
|
TRUE
|
FALSE
|
|
rs1491690
|
3
|
70131341
|
0
|
TRUE
|
FALSE
|
|
rs4435599
|
10
|
42390234
|
0
|
TRUE
|
FALSE
|
|
rs190316617
|
11
|
1797388
|
0
|
TRUE
|
TRUE
|
|
rs148035207
|
16
|
6330954
|
0
|
TRUE
|
FALSE
|
|
rs73157943
|
22
|
25333267
|
0
|
TRUE
|
FALSE
|
Summarization report parameters
|
Parameter
|
Value
|
|
chromosome_col
|
CHR
|
|
position_col
|
POS
|
|
ref_allele_col
|
Non_Effect_Allele
|
|
alt_allele_col
|
Effect_Allele
|
|
allele_freq_col
|
AF
|
|
beta_interaction_col
|
Beta_Interaction_1
|
|
p_interaction_col
|
P_Value_Interaction
|
|
p_joint_col
|
P_Value_Joint
|
|
p_marginal_col
|
P_Value_Marginal
|
|
gw_threshold
|
5e-8
|
|
prune_threshold_int
|
1e-5
|
|
prune_threshold_joint
|
5e-8
|
|
prune_locus_width
|
500000
|
|
GEM_file
|
sex_int_res_full
|
|
variant_id_col
|
RSID
|
|
maf_filter
|
0.05
|
